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NEW YORK | In this confounding start to the 2009 season - when the Washington Nationals have already spent plenty of nights dissecting games they could have and probably should have won - three themes have emerged as early-warning signs of why they continue to have nights like Friday.

Their hitting with runners in scoring position has left them grasping at thin air at the worst times. Their bullpen, in two configurations, hasn’t shown a consistent ability to get through innings. And their defense, viewed through the prism of spring training optimism as improved, has continued to give extra outs to opposing offenses with errors and misplays.

When two of those three conditions are present, the Nationals usually don’t win. Especially with a pitcher like Johan Santana on the mound.

All three were there Friday night.

The Nationals came within a run on two occasions, only to miss an opportunity to take the lead with Santana still in the game in the sixth. Their bullpen walked five batters, and reliever Kip Wells allowed an insurance run that became the difference in the Mets’ 4-3 win. And their defense made just enough mistakes to sustain a Mets offense that squandered plenty of its own chances to dent Nationals starter Scott Olsen.

“This is a game like some of the ones earlier where we gave a good team a handful of extra outs, and you can’t afford to do that,” right fielder Austin Kearns said.

So despite an impressive effort from Olsen, who allowed two earned runs in six innings and gave the the team its fourth consecutive quality start, the Nationals lost for the fifth time in seven games.

In all of those games, they either had the lead in the ninth inning or lost by a run.

“Losing’s frustrating, whether it’s me, one of the other starters or any of the bullpen guys,” Olsen said. “I tried to do my best, and Santana outdid me. It happens.”

Santana gnashed his way through the Nationals’ order in the first four innings, striking out eight of the 14 batters he faced. He paid a price for all those strikeouts, though, in the form of an elevated pitch count that took some of the zip off his fastball by the fifth inning. The Nationals got two hits off him in the fifth, and had runners on first and second with no outs in the sixth after Ryan Zimmerman and Adam Dunn followed Nick Johnson’s home run with a walk and a single, respectively.

And only Johnson’s homer produced a run. While the first baseman poked a Santana fastball to left for a 340-foot homer, the Nationals were otherwise done in by a dearth of clutch hitting.

Most odious was the chance they squandered in the sixth inning, with the tying run at second and none out against a tiring Santana. But the left-hander pumped four straight fastballs to strike out Elijah Dukes, then baited Kearns with four before putting him away with a vintage Santana changeup.

“Opportunities like that don’t come very often,” Dunn said. “It’s nothing we did wrong. He was really good today.”

But the outfielders’ sixth-inning strikeouts weren’t the only instance where they hampered Washington’s chances of winning.

Dukes hesitated while charging a Carlos Beltran liner in the third inning, diving too late to prevent it from going under his glove and skittering to the wall as Luis Castillo scored. Kearns had his own problems in the sixth, diving late for a Fernando Tatis liner that got away from him and rolled to the right-field corner.

“I thought I had a play on it, and then when I started diving, I knew I wasn’t going to get it, so I tried to just kind of swat at it and knock it down, so it wouldn’t do that,” Kearns said. “That didn’t work.”

That, plus the Mets’ eighth-inning run, rendered Jesus Flores’ two-run homer in the ninth moot, when it could have been the blast that put Washington ahead, if not for the same issues that came up again Friday night.

“It’s never been the lack of effort. They don’t roll over,” manager Manny Acta said. “That’s a good part of it, but you still have to win some games.”